Contacts of the helix formed by residues 207 - 222 (chain B) in PDB entry 1W98
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199B ALA* 4.3 2.5 - - - -
206B CYS* 1.3 76.2 - - - +
208B GLY* 1.3 64.5 + - - +
209B ASP* 3.9 7.8 + - - +
210B GLU* 2.5 42.8 + - - +
211B ILE* 3.1 24.0 + - - +
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Residues in contact with GLY 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B LEU* 3.8 33.0 - - - +
196B HIS* 6.1 0.4 - - - -
199B ALA* 4.0 14.3 - - - +
207B SER* 1.3 72.1 - - - +
209B ASP* 1.3 56.5 + - - +
211B ILE* 3.1 5.8 + - - +
212B LEU* 2.9 30.4 + - - +
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Residues in contact with ASP 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B SER* 3.2 8.8 + - - +
208B GLY* 1.3 74.7 - - - +
210B GLU* 1.3 58.0 + - + +
212B LEU* 3.5 20.2 - - - +
213B THR* 3.0 31.7 + - - -
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Residues in contact with GLU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B LEU* 3.7 28.0 - - + +
205B ALA 4.5 8.1 - - - +
206B CYS* 4.1 4.9 - - - +
207B SER* 2.5 40.2 + - - +
209B ASP* 1.3 78.1 - - + +
211B ILE* 1.3 59.1 + - - +
213B THR* 3.4 7.5 + - - +
214B MET* 3.0 30.5 + - - +
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Residues in contact with ILE 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B LEU* 4.0 5.8 - - + -
178B ILE* 3.7 29.6 - - + +
179B SER* 3.6 18.8 + - - +
182B PHE* 3.4 38.4 - - + -
195B LEU* 3.6 11.2 - - + -
198B PHE* 4.1 4.3 - - + +
199B ALA* 4.0 31.4 - - + +
206B CYS* 4.1 7.9 - - + -
207B SER 3.1 18.1 + - - +
208B GLY* 3.1 7.4 + - - +
210B GLU* 1.3 73.5 - - - +
212B LEU* 1.3 54.8 + - - +
214B MET 3.4 0.2 + - - -
215B GLU* 2.8 34.5 + - - +
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Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLU 5.8 3.6 - - - +
41A THR 5.8 1.3 - - - +
43A GLY* 3.8 31.0 - - - +
182B PHE* 4.0 10.5 - - + -
195B LEU* 3.5 38.1 - - + -
208B GLY 2.9 13.5 + - - +
209B ASP* 3.5 26.9 - - - +
211B ILE* 1.3 77.2 - - - +
213B THR* 1.3 62.4 + - - +
215B GLU* 3.4 20.3 - - - +
216B LEU* 3.6 15.0 + - + +
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Residues in contact with THR 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B ASP 3.0 19.1 + - - -
210B GLU* 3.7 7.6 - - - -
211B ILE 3.4 0.4 - - - -
212B LEU* 1.3 75.9 - - - +
214B MET* 1.3 64.5 + - - +
216B LEU* 3.4 11.0 + - - +
217B MET* 3.2 35.5 + - + +
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Residues in contact with MET 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B TYR* 4.3 7.0 - - - +
172B LEU* 4.0 13.7 - - + -
175B LEU* 3.7 30.5 - - + +
176B ILE* 3.7 27.6 - - + -
179B SER* 3.5 27.4 - - - +
210B GLU 3.0 18.5 + - - +
213B THR* 1.3 74.1 - - - +
215B GLU* 1.3 65.8 + - - +
216B LEU 3.1 1.6 - - - -
217B MET* 3.1 36.5 + - + +
218B ILE* 2.9 38.3 + - + +
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Residues in contact with GLU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLY* 3.7 17.8 - - - -
44A VAL* 3.8 8.7 + - - +
179B SER* 4.2 7.5 - - - +
182B PHE* 3.6 15.6 - - + -
183B ILE* 3.6 30.3 - - + +
186B LYS* 2.6 38.9 + - - -
211B ILE 2.8 18.9 + - - +
212B LEU* 3.4 16.6 - - - +
214B MET* 1.3 73.8 - - - +
216B LEU* 1.3 62.7 + - + +
218B ILE* 3.5 1.3 + - - +
219B MET* 2.9 48.0 + - + +
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 4.0 16.2 - - + -
44A VAL* 4.0 26.7 - - + -
71A HIS* 3.5 48.5 - - + +
76A LEU* 4.6 10.3 - - + -
212B LEU 3.6 14.1 + - - +
213B THR* 3.4 11.6 + - - +
214B MET 3.1 0.6 - - - -
215B GLU* 1.3 84.8 - - + +
217B MET* 1.3 62.8 + - + +
219B MET* 4.0 2.6 - - - -
220B LYS* 3.0 35.3 + - + +
224B TRP* 4.7 9.6 - - + -
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Residues in contact with MET 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B TYR* 3.4 26.0 - - - +
165B GLN* 5.5 2.5 - - - +
172B LEU* 6.0 2.2 - - + -
213B THR* 3.2 33.0 + - + +
214B MET* 3.1 36.2 + - + +
216B LEU* 1.3 76.4 - - + +
218B ILE* 1.3 55.3 + - - +
220B LYS* 3.5 9.3 + - - +
221B ALA* 2.9 32.9 + - - +
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Residues in contact with ILE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B PHE* 4.5 10.1 - - + -
161B TYR* 3.7 30.2 - - + -
176B ILE* 3.4 29.4 - - + +
179B SER* 3.9 3.6 - - - -
180B SER* 3.5 17.9 - - - +
183B ILE* 3.6 16.8 - - + -
214B MET* 2.9 40.1 + - + +
215B GLU 3.8 3.1 - - - +
217B MET* 1.3 74.0 - - - +
219B MET* 1.3 64.9 + - + +
221B ALA* 3.2 2.8 + - - +
222B LEU* 2.9 45.4 + - + +
226B LEU* 5.5 0.2 - - + -
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Residues in contact with MET 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 3.9 27.6 - - + -
49A ILE* 3.9 10.3 - - + -
183B ILE* 3.7 26.7 - - + -
215B GLU* 2.9 44.0 + - + +
216B LEU* 4.2 3.4 - - - +
218B ILE* 1.3 71.3 - - - +
220B LYS* 1.3 59.4 - - - +
222B LEU 3.3 1.7 + - - -
223B LYS 3.2 2.9 + - - -
224B TRP* 2.8 71.2 + - + -
226B LEU* 3.6 31.2 - - + -
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Residues in contact with LYS 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A HIS* 2.7 51.9 + - + +
73A GLU* 4.9 3.2 + - - -
216B LEU* 3.0 30.1 + - + +
217B MET* 4.1 8.1 - - - +
219B MET* 1.3 74.7 - - - +
221B ALA* 1.3 59.2 + - - +
223B LYS* 3.0 27.5 + - - +
224B TRP* 4.2 25.4 - - + +
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Residues in contact with ALA 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B TYR* 3.6 28.0 - - + -
164B THR* 3.7 26.9 - - - +
165B GLN* 4.4 4.7 - - - +
217B MET 2.9 19.1 + - - +
220B LYS* 1.3 78.9 - - - +
222B LEU* 1.3 59.2 + - - +
223B LYS* 3.2 10.7 + - - +
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Residues in contact with LEU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B PHE* 4.1 24.0 - - + +
160B ARG* 3.7 35.5 + - + +
161B TYR* 3.6 30.5 - - + +
164B THR* 4.8 3.1 - - + -
218B ILE* 2.9 34.4 + - + +
219B MET 3.9 3.6 - - - +
220B LYS 3.2 0.2 - - - -
221B ALA* 1.3 79.0 - - - +
223B LYS* 1.3 70.8 + - - +
224B TRP 4.3 0.2 - - - +
225B ARG* 3.2 21.4 + - - +
226B LEU* 3.7 25.8 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il